绵羊线粒体DNA的父系遗传

通过多赛特公羊与小尾寒羊杂交家系(Pmt家系)mtDNA D-loop PCR-RFLP和重复序列区扩增进行的分子长度多态分析发现, 该家系存在mtDNA父系遗传现象, 通过D-loop 5'端PCR-SSCP分析也发现了该家系的父系遗传现象, 提示绵羊(Ovis aries)存在mtDNA的父系遗传, 进而对mtDNA父系遗传的机制进行了讨论.     

线粒体疾病与核基因－线粒体基因的表达调控

线粒体与疾病是当前生物医学领域最前沿之一。本文简单介绍线粒体生物医学的基础知识、线粒体疾病的遗传模式,综述了近年来在线粒体DNA（mtDNA）突变和疾病、核基因突变和疾病等领域的研究进展,着重阐明核基因（特别是核修饰基因）调控mtDNA突变致病表达的分子机制。     

马鹿线粒体DNA研究新进展

线粒体DNA作为理想的分子遗传标记被广泛应用于马鹿进化生物学、种群遗传学和保护生物学的研究.该文阐述了mtDNA在马鹿中的研究进展,重点介绍马鹿mtDNA序列的研究概况及其多态性在马鹿物种识别、起源和进化、地理分化、遗传多样性和保护管理等方面的应用情况.     

中国内蒙古鄂伦春族线粒体DNA高变区Ⅰ和高变区Ⅱ遗传多态性

收集50份鄂伦春族无关人群外周血样本, 用ABI PRISM377测序仪对其mtDNA HVRⅠ和HVRⅡ进行测序, 计算多态性位点数、单倍型数目、单倍型频率、平均核苷酸差异数目等多态性指标; 结合已发表的其他民族mtDNA遗传资料, 根据Nei法计算鄂伦春族与各群体之间的遗传距离, 进行聚类分析, 绘制系统发生树。鄂伦春族群体mtDNA两个高变区与CRS序列比对, 分别发现52和24个多态性位点, 分别界定了38和27种单倍型, 单倍型多态性分别为0.964±0.018和0.929±0.019; 平均核苷酸差异分别为7.379和2.408; 用HVRⅠ序列多态性数据计算Fst和dA两种遗传距离, 相关系数r为0.993(P<0.01); 基于HVRⅠ序列的系统树显示鄂伦春族与中国台湾、南方汉族和中国香港人群遗传距离较近, 与北方汉族、蒙古族及其国外人群遗传距离相对较远。我国鄂伦春族人群mtDNA具有相对独特的遗传特征, 其遗传多态性和个体识别力较高, 可用于民族起源、迁徙、法医学个体识别等领域研究。     

双孢蘑菇杂交菌株As2796家系的分子遗传研究

应用PCR和凝胶电泳等技术,对双孢蘑菇杂交菌株As2796及其亲本和子代作分子遗传标记跟踪分析,结果如下：1）总DNA的RAPD分析表明,随着遗传代数的增加,杂种子代和出发异核体亲本间的遗传差异逐渐增大;2）mtDNA的酶切图谱表明,亲本8213及其杂交子代具有相同的基因型,表明双孢蘑菇mtDNA呈单亲遗传;3）Est同工酶的PAGE图谱表明,结合了亲本02高产特征和8213优质特征的杂交子代具有两个亲本的标记带型,证明Est同工酶标记是双孢蘑菇新菌株特性预测或鉴定的有效指标。     

线粒体DNA遗传特性的研究新进展

结合传统的线粒体DNA遗传特性理论与该领域的最新研究成果,从mtDNA的结构、组织特异性、母系遗传、进化速率及其与核基因组的相互关系等方面做了简要综述。同时,对今后的研究工作提出了一些建议。     

线粒体DNA多态性在海洋动物群体遗传结构研究中的应用

线粒体DNA( mtDNA)分析在揭示物种亲缘关系、遗传比较、系统进化和遗传结构等领域的研究中得到了广泛的应用,尤其是在海洋动物的遗传结构研究中发挥了重要的作用.介绍线粒体DNA的结构特征、多态性研究方法,并对其在海洋动物群体遗传结构研究中的应用进行了综述.     

动物线粒体DNA重组的研究进展

动物线粒体DNA作为遗传标记广泛用于从种内到高级阶元的许多生物学领域,这些应用是建立在线粒体DNA的严格母系遗传方式和不发生重组的基础上的。近年来的研究提出了一些能够证明动物mtDNA发生重组的直接和间接证据。动物mtDNA重组可能主要通过两条途径发生,一条途径是母系mtDNA与核基因组中mtDNA假基因间发生重组;另一条途径是通过父系渗漏引起的不同单倍型的双亲mtDNA间发生重组。父系渗漏是最可能的途径。如果动物界广泛存在线粒体DNA重组,将会对以mtDNA严格母系遗传为基础的许多应用领域产生重要影响。     

牦牛分子遗传多样性研究进展

遗传多样性研究可有效地揭示牦牛的遗传变异, 是牦牛群体遗传学研究的主要内容之一。自20世纪70年代以来, 人们已对牦牛的体形外貌特征、染色体核型(带型)、生理生化特性和DNA序列变异等进行了较为深入地研究。随着分子遗传学和DNA测序技术的迅猛发展, 近年来的研究主要集中在牦牛的分子遗传多样性。文章对近15年来牦牛mtDNA和核基因组分子标记及侯选基因多样性的研究现状进行了综述, 对前景进行展望, 以期为牦牛群体基因组学等研究提供依据。     

高血压相关的线粒体DNA突变

线粒体DNA(mtDNA)突变是高血压发病的分子机制之一。已经报道的与原发性高血压相关的mtDNA突变包括:tRNAMet A4435G,tRNAMet/tRNAGln A4401G,tRNAIle A4263G,T4291C和A4295G突变。这些高血压相关的mtDNA突变改变了相应的线粒体tRNA的结构,导致线粒体tRNA的代谢障碍。而线粒体tRNAs的代谢缺陷则影响蛋白质合成,造成氧化磷酸化缺陷,降低ATP的合成,增加活性氧的产生。因此,线粒体的功能缺陷可能在高血压的发生发展中起一定的作用。mtDNA突变发病的组织特异性则可能与线粒体tRNAs的代谢以及核修饰基因相关。目前发现的这些高血压相关的mtDNA突变则应该作为今后高血压诊断的遗传风险因子。高血压相关的线粒体功能缺陷的深入研究也将进一步诠释母系遗传高血压的分子致病机制,为高血压的预防、控制和治疗提供依据。文章对高血压相关的mtDNA突变进行了综述。     

青蟹线粒体COI假基因的分离和特征分析

线粒体DNA标记在遗传结构和系统进化研究中得到广泛应用,然而核假基因的存在对此有很大威胁。本文以中国东南沿海的青蟹(Scylla paramamosain)为研究对象,利用线粒体COI基因的通用引物和特异性引物进行扩增,分别得到34个假基因（nuclear mitochondrial pseudogenes, Numts）和5个线粒体COI基因序列。在所获得的34个假基因中共定义了29种单倍型,根据序列的相似度,这些假基因可以分为2类,每类假基因都有各自保守的核苷酸序列。第Ⅰ类假基因存在2处插入序列和1处8 bp的缺失序列,这些位点导致了整个阅读框的移位;在第Ⅱ类假基因和5个线粒体COI序列中只有碱基替换,未发现插入和缺失序列。实验结果分析表明,这两类假基因分别代表了2次核整合事件,即核转移事件的最低值。研究结果提示了     

Amplification of multiple copies of mitochondrial Cytochrome b gene fragments in the Australian freshwater crayfish,Cherax destructor Clark (Parastacidae: Decapoda)

Non-coding copies of fragments of the mitochondrial genome translocated to the nucleus or pseudogenes are being found with increasing frequency in a diversity of organisms. As part of a study to evaluate the utility of a range of mitochondrial gene regions for population genetic and systematic studies of the Australian freshwater crayfish, Cherax destructor (the yabby), we report the first detection of Cytochrome b (Cyt b) pseudogenes in crustaceans. We amplified and sequenced fragments of the mitochondrial Cyt b gene from 14 individuals of C. destructor using polymerase chain reaction (PCR) with primers designed from conserved regions of Penaeus monodon and Drosophila melanogaster mitochondrial genomes. The phylogenetic tree produced from the amplified fragments using these primers showed a very different topology to the trees obtained from sequences from three other mitochondrial genes, suggesting one or more nuclear pseudogenes have been amplified. Supporting this conclusion, two highly divergent sequences were isolated from each of two single individuals, and a 2 base pair (bp) deletion in one sequence was observed. There was no evidence to support inadvertent amplification of parasite DNA or contamination of samples from other sources. These results add to other recent observations of pseudogenes suggesting the frequent transfer of mitochondrial DNA (mtDNA) genes to the nucleus and reinforces the necessity of great care in interpreting PCR-generated Cyt b sequences used in population or evolutionary studies in freshwater crayfish and crustaceans more generally.     

Frequent assimilation of mitochondrial DNA by grasshopper nuclear genomes

Multiple copies of mitochondrial-like DNA were found in the brown mountain grasshopper, Podisma pedestris (Orthoptera: Acrididae), paralogous to COI and ND5 regions. The same was discovered using the ND5 regions of nine other grasshopper species from four separate subfamilies (Podisminae, Calliptaminae, Cyrtacanthacridinae, and Gomphocerinae). The extra ND5-like sequences were shown to be nuclear in the desert locust, Schistocerca gregaria (Cyrtacanthacridinae), and probably so in P. pedestris and an Italopodisma sp. (Podisminae). Eighty-seven different ND5-like nuclear mitochondrial pseudogenes (Numts) were sequenced from 12 grasshopper individuals. Different nuclear mitochondrial pseudogenes, if descended from the same mitochondrial immigrant, will have diverged from each other under no selective constraints because of their loss of functionality. Evidence of selective constraints in the differences between any two Numt sequences (e.g., if most differences are at third positions of codons) implies that they have separate mitochondrial origins. Through pairwise comparisons of pseudogene sequences, it was established that there have been at least 12 separate mtDNA integrations into P. pedestris nuclear genomes. This is the highest reported rate of horizontal transfer between organellar and nuclear genomes within a single animal species. The occurrence of numerous mitochondrial pseudogenes in nuclear genomes derived from separate integration events appears to be a common phenomenon among grasshoppers. More than one type of mechanism appears to have been involved in generating the observed grasshopper Numts.     

Novel miniature transposable elements in thermophilic Synechococcus strains and their impact on an environmental population

The genomes of the two closely related freshwater thermophilic cyanobacteria Synechococcus sp. strain JA-3-3Ab and Synechococcus sp. strain JA-2-3B′a(2-13) each host several families of insertion sequences (ISSoc families) at various copy numbers, resulting in an overall high abundance of insertion sequences in the genomes. In addition to full-length copies, a large number of internal deletion variants have been identified. ISSoc2 has two variants (ISSoc2∂-1 and ISSoc2∂-2) that are observed to have multiple near-exact copies. Comparison of environmental metagenomic sequences to the Synechococcus genomes reveals novel placement of copies of ISSoc2, ISSoc2∂-1, and ISSoc2∂-2. Thus, ISSoc2∂-1 and ISSoc2∂-2 appear to be active nonautonomous mobile elements derived by internal deletion from ISSoc2. Insertion sites interrupting genes that are likely critical for cell viability were detected; however, most insertions either were intergenic or were within genes of unknown function. Most novel insertions detected in the metagenome were rare, suggesting a stringent selective environment. Evidence for mobility of internal deletion variants of other insertion sequences in these isolates suggests that this is a general mechanism for the formation of miniature insertion sequences.     

Periodic extinctions of transposable elements in bacterial lineages: evidence from intragenomic variation in multiple genomes

Most previous work on the evolution of mobile DNA was limited by incomplete sequence information. Whole genome sequences allow us to overcome this limitation. I study the nucleotide diversity of prominent members of five insertion sequence families whose transposition activity is encoded by a single transposase gene. Eighteen among 376 completely sequenced bacterial genomes and plasmids carry between 3 and 20 copies of a given insertion sequence. I show that these copies generally show very low DNA divergence. Specifically, more than 68% of the transposase genes are identical within a genome. The average number of amino acid replacement substitutions at amino acid replacement sites is Ka = 0.013, that at silent sites is Ks = 0.1. This low intragenomic diversity stands in stark contrast to a much higher divergence of the same insertion sequences among distantly related genomes. Gene conversion among protein-coding genes is unlikely to account for this lack of diversity. The relation between transposition frequencies and silent substitution rates suggests that most insertion sequences in a typical genome are evolutionarily young and have been recently acquired. They may undergo periodic extinction in bacterial lineages. By implication, they are detrimental to their host in the long run. This is also suggested by the highly skewed and patchy distribution of insertion sequences among genomes. In sum, one can think of insertion sequences as slow-acting infectious diseases of cell lineages.     

Mitochondrial pseudogenes are pervasive and often insidious in the snapping shrimp genus Alpheus

Here we show that multiple DNA sequences, similar to the mitochondrial cytochrome oxidase I (COI) gene, occur within single individuals in at least 10 species of the snapping shrimp genus Alpheus. Cloning of amplified products revealed the presence of copies that differed in length and (more frequently) in base substitutions. Although multiple copies were amplified in individual shrimp from total genomic DNA (gDNA), only one sequence was amplified from cDNA. These results are best explained by the presence of nonfunctional duplications of a portion of the mtDNA, probably located in the nuclear genome, since transfer into the nuclear gene would render the COI gene nonfunctional due to differences in the nuclear and mitochondrial genetic codes. Analysis of codon variation suggests that there have been 21 independent transfer events in the 10 species examined. Within a single animal, differences between the sequences of these pseudogenes ranged from 0.2% to 20.6%, and those between the real mtDNA and pseudogene sequences ranged from 0.2% to 18.8% (uncorrected). The large number of integration events and the large range of divergences between pseudogenes and mtDNA sequences suggest that genetic material has been repeatedly transferred from the mtDNA to the nuclear genome of snapping shrimp. Unrecognized pseudogenes in phylogenetic or population studies may result in spurious results, although previous estimates of rates of molecular evolution based on Alpheus sister taxa separated by the Isthmus of Panama appear to remain valid. Especially worrisome for researchers are those pseudogenes that are not obviously recognizable as such. An effective solution may be to amplify transcribed copies of protein-coding mitochondrial genes from cDNA rather than using genomic DNA.     

Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders

Extensive gene rearrangement is reported in the mitochondrial genomes of lungless salamanders (Plethodontidae). In each genome with a novel gene order, there is evidence that the rearrangement was mediated by duplication of part of the mitochondrial genome, including the presence of both pseudogenes and additional, presumably functional, copies of duplicated genes. All rearrangement-mediating duplications include either the origin of light-strand replication and the nearby tRNA genes or the regions flanking the origin of heavy-strand replication. The latter regions comprise nad6, trnE, cob, trnT, an intergenic spacer between trnT and trnP and, in some genomes, trnP, the control region, trnF, rrnS, trnV, rrnL, trnL1, and nad1. In some cases, two copies of duplicated genes, presumptive regulatory regions, and/or sequences with no assignable function have been retained in the genome following the initial duplication; in other genomes, only one of the duplicated copies has been retained. Both tandem and nontandem duplications are present in these genomes, suggesting different duplication mechanisms. In some of these mitochondrial DNAs, up to 25% of the total length is composed of tandem duplications of noncoding sequence that includes putative regulatory regions and/or pseudogenes of tRNAs and protein-coding genes along with the otherwise unassignable sequences. These data indicate that imprecise initiation and termination of replication, slipped-strand mispairing, and intramolecular recombination may all have played a role in generating repeats during the evolutionary history of plethodontid mitochondrial genomes.     

A cryptic, intergeneric cytochrome c oxidase I pseudogene in tyrant flycatchers (family: Tyrannidae)

Nuclear mitochondrial pseudogenes, or "numts", are nonfunctional copies of mitochondrial genes that have been translocated to the nuclear genome. Numts have been used to study differences in mutation rates between the nuclear and mitochondrial genomes, but have also been implicated as troublesome for phylogenetic studies and DNA-based species identification (i.e., DNA barcoding). In this study, a suspected numt discovered during a study of mitochondrial cytochrome c oxidase I (COI) diversity in North American birds was targeted and sequenced from tyrant flycatchers (family: Tyrannidae). In total, the numt was found in five taxa representing two genera. Substitution rates were compared between COI and numt sequences. None of the numt sequences harboured stop codons nor frameshift mutations, but phylogenetic analysis revealed they had accumulated more amino acid substitutions than the mitochondrial COI sequences. Mitochondrial COI appeared to be preferentially amplified in most cases, but methods for numt detection are discussed for cases like this where sequences lack obvious features for identification. Because of its persistence across a broad taxonomic lineage, this numt could form a valuable model system for studying evolution in numts. The full size of the numt and its location within the nuclear genome are yet to be determined.     

Fugu genome does not contain mitochondrial pseudogenes

Contrary to previous observations that fish genomes are devoid of nuclear mitochondrial pseudogenes, a genome-wide survey identified a large number of "recent" and "ancient" nuclear mitochondrial DNA fragments (Numts) in the whole-genome sequences of the fugu (Takifugu rubripes), Tetraodon nigroviridis, and zebrafish (Danio rerio). We have analyzed the latest assembly (v4.0) of the fugu genome and show that, like the Anopheles genome, the fugu nuclear genome does not contain mitochondrial pseudogenes. Fugu assembly v4.0 contains a single scaffold representing the near complete sequence of the fugu mitochondria. The "recent" Numts identified by the previous study in fugu assembly v2.0 are in fact shotgun sequences of mitochondrial DNA that were misassembled with the nuclear sequences, whereas the "ancient" Numts appear to be the result of spurious matches. It is likely that the Numts identified in the genomes of Tetraodon and zebrafish are also similar artifacts. Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification.